Study: Genome-wide and candidate gene association study of cigarette smoking behaviors. [PMID:19247474]
First author: Caporaso N
Journal: PLoS One
Date: 02/27/2009
Phenotype: Smoking behavior
Study population: 4,611 individuals (2,617 smokers)
Association P-value: 9 x 10-06
Odds ratio [95% confidence interval]: .08 [NR] fewer years
Gene: FAT4 - INTU
Minor allele frequency (controls): 0.39
rs950063
Position: chr4:126,431,919
(Open in UCSC Genome Browser)
Distance to nearest TSS: 242,030 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium threshold:
- In all HapMap 2 populations: r2≥0.8 r2≥0.9 r2=1.0
- In the HapMap 2 CEU population r2≥0.8 r2≥0.9 r2=1.0
SNPs in the linkage disequilibrium region sorted by decreasing amount of evidence supporting a functional role for the SNP:
rs12643736
Position: chr4:126,426,962
(Open in UCSC Genome Browser)
Distance to lead SNP: 4,957 bp
Distance to nearest TSS: 246,987 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.564
rs13114827
Position: chr4:126,431,339
(Open in UCSC Genome Browser)
Distance to lead SNP: 580 bp
Distance to nearest TSS: 242,610 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.635 / JPT: D'=1.0, r2=0.744 / YRI: D'=1.0, r2=1.0
rs13102120
Position: chr4:126,433,549
(Open in UCSC Genome Browser)
Distance to lead SNP: 1,630 bp
Distance to nearest TSS: 240,400 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.677
rs1506352
Position: chr4:126,431,057
(Open in UCSC Genome Browser)
Distance to lead SNP: 862 bp
Distance to nearest TSS: 242,892 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0
rs11726294
Position: chr4:126,430,330
(Open in UCSC Genome Browser)
Distance to lead SNP: 1,589 bp
Distance to nearest TSS: 243,619 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.534
rs10007099
Position: chr4:126,431,574
(Open in UCSC Genome Browser)
Distance to lead SNP: 345 bp
Distance to nearest TSS: 242,375 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.667 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.665
rs1506365
Position: chr4:126,468,333
(Open in UCSC Genome Browser)
Distance to lead SNP: 36,414 bp
Distance to nearest TSS: 205,616 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0
rs12639834
Position: chr4:126,426,695
(Open in UCSC Genome Browser)
Distance to lead SNP: 5,224 bp
Distance to nearest TSS: 247,254 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.545 / JPT: D'=1.0, r2=0.696
rs2174591
Position: chr4:126,433,736
(Open in UCSC Genome Browser)
Distance to lead SNP: 1,817 bp
Distance to nearest TSS: 240,213 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0
Credits:This resource uses data from:
- The NHGRI GWAS catalog (accessed August 10, 2011)
- The ENCODE project
- RegulomeDB
- The HapMap project
RegulomeDB (TM) Copyright ©2011 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. The RegulomeDB project at Stanford University is supported by a Genome Research Resource Grant from the US National Human Genome Research Institute, part of the US National Institutes of Health.